To unpack this mystery, you need to follow the chain from
tool_conf.xml (that's what the tool menu is made from) to the actual
tool directory and xml file name - eg:
rerla@rosst61:~/rgalaxy$ grep -i group tool_conf.xml
..
<tool file="stats/grouping.xml"/>
..
That means you need to look in [galaxyroot]/tools/stats for
grouping.xml to understand what the tool menu entry is going to do.
The actual command is found in the first few lines of the tool xml
file:
rerla@rosst61:~/rgalaxy$ head tools/stats/grouping.xml
<tool id="Grouping1" name="Group" version="1.9.4">
<description>data by a column and perform aggregate operation on
other columns.</description>
grouping.py
$out_file1
....
so the python script you want is in /tools/stats/grouping.py - I'd be
surprised if that's AWOL from a fresh mercurial clone?
Now for the harder part: unfortunately the error message was missing,
but my first guess is that your Python does not (yet) have rpy
installed.
There's a slew of dependencies described at
https://bitbucket.org/galaxy/galaxy-central/wiki/ToolDependencies
I hope this helps?
--
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;